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- PDB-4z90: ELIC bound with the anesthetic isoflurane in the resting state -

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Basic information

Entry
Database: PDB / ID: 4z90
TitleELIC bound with the anesthetic isoflurane in the resting state
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsTRANSPORT PROTEIN / ELIC / isoflurane / inhibition / anesthetics / resting state
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-4LE / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChen, Q. / Kinde, M. / Arjunan, P. / Cohen, A. / Xu, Y. / Tang, P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM056257 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM066358 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM049202 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM075770 United States
CitationJournal: Sci Rep / Year: 2015
Title: Direct Pore Binding as a Mechanism for Isoflurane Inhibition of the Pentameric Ligand-gated Ion Channel ELIC.
Authors: Chen, Q. / Kinde, M.N. / Arjunan, P. / Wells, M.M. / Cohen, A.E. / Xu, Y. / Tang, P.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,48024
Polymers368,79010
Non-polymers2,69014
Water7,566420
1
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,74012
Polymers184,3955
Non-polymers1,3457
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26880 Å2
ΔGint-127 kcal/mol
Surface area67020 Å2
MethodPISA
2
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,74012
Polymers184,3955
Non-polymers1,3457
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26890 Å2
ΔGint-129 kcal/mol
Surface area66980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.848, 267.079, 111.128
Angle α, β, γ (deg.)90.00, 106.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gamma-aminobutyric-acid receptor subunit beta-1


Mass: 36879.000 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria)
Strain: 3937 / Gene: Dda3937_00520 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4
#2: Chemical
ChemComp-4LE / (2R)-2-chloro-2-(difluoromethoxy)-1,1,1-trifluoroethane


Mass: 184.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2ClF5O
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: isoflurane, PEG 4000, ammonium sulfate, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→39.63 Å / Num. obs: 117464 / % possible obs: 99.9 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.251 / Net I/σ(I): 14.9
Reflection shellResolution: 3→3.16 Å / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHENIX1.9_1692refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RQU

3rqu


Resolution: 3→36.973 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 5880 5.02 %
Rwork0.209 --
obs0.2107 117183 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→36.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25270 0 160 420 25850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01426106
X-RAY DIFFRACTIONf_angle_d1.32835572
X-RAY DIFFRACTIONf_dihedral_angle_d13.3119444
X-RAY DIFFRACTIONf_chiral_restr0.0693924
X-RAY DIFFRACTIONf_plane_restr0.0074520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.38651640.37533528X-RAY DIFFRACTION96
3.0341-3.06980.37571930.33463715X-RAY DIFFRACTION100
3.0698-3.10720.35741970.31313734X-RAY DIFFRACTION100
3.1072-3.14650.35282010.30133669X-RAY DIFFRACTION100
3.1465-3.18790.32451840.29023729X-RAY DIFFRACTION100
3.1879-3.23150.30032290.29053678X-RAY DIFFRACTION100
3.2315-3.27770.32542030.28973695X-RAY DIFFRACTION100
3.2777-3.32660.31651930.28563724X-RAY DIFFRACTION100
3.3266-3.37850.32141820.27743723X-RAY DIFFRACTION100
3.3785-3.43390.30611930.26723713X-RAY DIFFRACTION100
3.4339-3.4930.31271950.26233744X-RAY DIFFRACTION100
3.493-3.55650.30171810.26933685X-RAY DIFFRACTION100
3.5565-3.62480.3232230.25443706X-RAY DIFFRACTION100
3.6248-3.69880.3082040.24933708X-RAY DIFFRACTION100
3.6988-3.77910.26551790.25083720X-RAY DIFFRACTION100
3.7791-3.86690.26911720.22553719X-RAY DIFFRACTION100
3.8669-3.96350.26692250.22593702X-RAY DIFFRACTION100
3.9635-4.07060.25792030.21683725X-RAY DIFFRACTION100
4.0706-4.19020.24031810.20443716X-RAY DIFFRACTION100
4.1902-4.32520.22231940.19293704X-RAY DIFFRACTION100
4.3252-4.47960.21321980.17493730X-RAY DIFFRACTION100
4.4796-4.65860.18022200.16763701X-RAY DIFFRACTION100
4.6586-4.87020.2051710.17043724X-RAY DIFFRACTION100
4.8702-5.12630.20782020.17593737X-RAY DIFFRACTION100
5.1263-5.44660.23132060.1793715X-RAY DIFFRACTION100
5.4466-5.86560.2051890.17873752X-RAY DIFFRACTION100
5.8656-6.4530.21791910.18683709X-RAY DIFFRACTION100
6.453-7.38030.24792030.19143735X-RAY DIFFRACTION100
7.3803-9.27410.17522000.15553750X-RAY DIFFRACTION100
9.2741-36.97620.23562040.20583713X-RAY DIFFRACTION99

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